Merge branch 'PythonImprovements' into pytest
This commit is contained in:
Martin Diehl
commit
ea4c4b6636
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@ -15,11 +15,6 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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def mostFrequent(arr):
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unique, inverse = np.unique(arr, return_inverse=True)
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return unique[np.argmax(np.bincount(inverse))]
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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@ -46,9 +41,8 @@ for name in filenames:
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geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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damask.util.croak(geom.update(ndimage.filters.generic_filter(
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geom.microstructure,mostFrequent,
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size=(options.stencil,)*3).astype(geom.microstructure.dtype)))
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damask.util.croak(geom.clean(options.stencil))
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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if name is None:
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@ -38,16 +38,6 @@ parser.set_defaults(reflect = False)
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(options, filenames) = parser.parse_args()
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if options.directions is None:
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parser.error('no direction given.')
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if not set(options.directions).issubset(validDirections):
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invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)]
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parser.error('invalid directions {}. '.format(*invalidDirections))
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limits = [None,None] if options.reflect else [-2,0]
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if filenames == []: filenames = [None]
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for name in filenames:
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@ -55,15 +45,7 @@ for name in filenames:
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geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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microstructure = geom.get_microstructure()
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if 'z' in options.directions:
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microstructure = np.concatenate([microstructure,microstructure[:,:,limits[0]:limits[1]:-1]],2)
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if 'y' in options.directions:
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microstructure = np.concatenate([microstructure,microstructure[:,limits[0]:limits[1]:-1,:]],1)
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if 'x' in options.directions:
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microstructure = np.concatenate([microstructure,microstructure[limits[0]:limits[1]:-1,:,:]],0)
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damask.util.croak(geom.update(microstructure,rescale=True))
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damask.util.croak(geom.mirror(options.directions,options.reflect))
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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if name is None:
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@ -2,6 +2,7 @@ import os
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from io import StringIO
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import numpy as np
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from scipy import ndimage
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import vtk
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from vtk.util import numpy_support
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@ -10,380 +11,426 @@ from . import version
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class Geom():
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"""Geometry definition for grid solvers."""
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"""Geometry definition for grid solvers."""
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def __init__(self,microstructure,size,origin=[0.0,0.0,0.0],homogenization=1,comments=[]):
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"""
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New geometry definition from array of microstructures and size.
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def __init__(self,microstructure,size,origin=[0.0,0.0,0.0],homogenization=1,comments=[]):
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"""
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New geometry definition from array of microstructures and size.
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Parameters
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----------
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microstructure : numpy.ndarray
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microstructure array (3D)
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size : list or numpy.ndarray
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physical size of the microstructure in meter.
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origin : list or numpy.ndarray, optional
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physical origin of the microstructure in meter.
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homogenization : integer, optional
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homogenization index.
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comments : list of str, optional
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comments lines.
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Parameters
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----------
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microstructure : numpy.ndarray
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microstructure array (3D)
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size : list or numpy.ndarray
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physical size of the microstructure in meter.
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origin : list or numpy.ndarray, optional
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physical origin of the microstructure in meter.
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homogenization : integer, optional
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homogenization index.
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comments : list of str, optional
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comments lines.
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"""
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self.__transforms__ = \
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self.set_microstructure(microstructure)
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self.set_size(size)
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self.set_origin(origin)
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self.set_homogenization(homogenization)
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self.set_comments(comments)
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def __repr__(self):
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"""Basic information on geometry definition."""
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return util.srepr([
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'grid a b c: {}'.format(' x '.join(map(str,self.get_grid ()))),
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'size x y z: {}'.format(' x '.join(map(str,self.get_size ()))),
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'origin x y z: {}'.format(' '.join(map(str,self.get_origin()))),
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'homogenization: {}'.format(self.get_homogenization()),
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'# microstructures: {}'.format(len(np.unique(self.microstructure))),
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'max microstructure: {}'.format(np.nanmax(self.microstructure)),
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])
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def update(self,microstructure=None,size=None,origin=None,rescale=False):
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"""
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Updates microstructure and size.
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Parameters
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----------
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microstructure : numpy.ndarray, optional
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microstructure array (3D).
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size : list or numpy.ndarray, optional
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physical size of the microstructure in meter.
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origin : list or numpy.ndarray, optional
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physical origin of the microstructure in meter.
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rescale : bool, optional
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ignore size parameter and rescale according to change of grid points.
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"""
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grid_old = self.get_grid()
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size_old = self.get_size()
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origin_old = self.get_origin()
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unique_old = len(np.unique(self.microstructure))
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max_old = np.nanmax(self.microstructure)
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if size is not None and rescale:
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raise ValueError('Either set size explicitly or rescale automatically')
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self.set_microstructure(microstructure)
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self.set_origin(origin)
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if size is not None:
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self.set_size(size)
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elif rescale:
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self.set_size(self.get_grid()/grid_old*self.size)
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message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))]
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if np.any(grid_old != self.get_grid()):
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message[-1] = util.delete(message[-1])
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message.append(util.emph('grid a b c: {}'.format(' x '.join(map(str,self.get_grid())))))
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message.append('size x y z: {}'.format(' x '.join(map(str,size_old))))
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if np.any(size_old != self.get_size()):
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message[-1] = util.delete(message[-1])
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message.append(util.emph('size x y z: {}'.format(' x '.join(map(str,self.get_size())))))
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message.append('origin x y z: {}'.format(' '.join(map(str,origin_old))))
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if np.any(origin_old != self.get_origin()):
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message[-1] = util.delete(message[-1])
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message.append(util.emph('origin x y z: {}'.format(' '.join(map(str,self.get_origin())))))
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message.append('homogenization: {}'.format(self.get_homogenization()))
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message.append('# microstructures: {}'.format(unique_old))
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if unique_old != len(np.unique(self.microstructure)):
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message[-1] = util.delete(message[-1])
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message.append(util.emph('# microstructures: {}'.format(len(np.unique(self.microstructure)))))
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message.append('max microstructure: {}'.format(max_old))
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if max_old != np.nanmax(self.microstructure):
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message[-1] = util.delete(message[-1])
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message.append(util.emph('max microstructure: {}'.format(np.nanmax(self.microstructure))))
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return util.return_message(message)
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def set_comments(self,comments):
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"""
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Replaces all existing comments.
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Parameters
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----------
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comments : list of str
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new comments.
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"""
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self.comments = []
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self.add_comments(comments)
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def add_comments(self,comments):
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"""
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Appends comments to existing comments.
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Parameters
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----------
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comments : list of str
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new comments.
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"""
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self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
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def set_microstructure(self,microstructure):
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"""
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Replaces the existing microstructure representation.
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Parameters
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----------
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microstructure : numpy.ndarray
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microstructure array (3D).
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"""
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if microstructure is not None:
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if len(microstructure.shape) != 3:
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raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape))
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elif microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
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raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype))
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else:
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self.microstructure = np.copy(microstructure)
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def set_size(self,size):
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"""
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Replaces the existing size information.
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Parameters
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----------
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size : list or numpy.ndarray
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physical size of the microstructure in meter.
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"""
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if size is None:
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grid = np.asarray(self.microstructure.shape)
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self.size = grid/np.max(grid)
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else:
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if len(size) != 3 or any(np.array(size)<=0):
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raise ValueError('Invalid size {}'.format(*size))
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else:
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self.size = np.array(size)
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def set_origin(self,origin):
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"""
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Replaces the existing origin information.
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Parameters
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----------
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origin : list or numpy.ndarray
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physical origin of the microstructure in meter
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"""
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if origin is not None:
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if len(origin) != 3:
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raise ValueError('Invalid origin {}'.format(*origin))
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else:
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self.origin = np.array(origin)
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def set_homogenization(self,homogenization):
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"""
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Replaces the existing homogenization index.
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Parameters
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----------
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homogenization : integer
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homogenization index
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"""
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if homogenization is not None:
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if not isinstance(homogenization,int) or homogenization < 1:
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raise TypeError('Invalid homogenization {}'.format(homogenization))
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else:
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self.homogenization = homogenization
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def get_microstructure(self):
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"""Return the microstructure representation."""
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return np.copy(self.microstructure)
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def get_size(self):
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"""Return the physical size in meter."""
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return np.copy(self.size)
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def get_origin(self):
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"""Return the origin in meter."""
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return np.copy(self.origin)
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def get_grid(self):
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"""Return the grid discretization."""
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return np.array(self.microstructure.shape)
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def get_homogenization(self):
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"""Return the homogenization index."""
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return self.homogenization
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def get_comments(self):
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"""Return the comments."""
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return self.comments[:]
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def get_header(self):
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"""Return the full header (grid, size, origin, homogenization, comments)."""
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header = ['{} header'.format(len(self.comments)+4)] + self.comments
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header.append('grid a {} b {} c {}'.format(*self.get_grid()))
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header.append('size x {} y {} z {}'.format(*self.get_size()))
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header.append('origin x {} y {} z {}'.format(*self.get_origin()))
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header.append('homogenization {}'.format(self.get_homogenization()))
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return header
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"""
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self.__transforms__ = \
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self.set_microstructure(microstructure)
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self.set_size(size)
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self.set_origin(origin)
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self.set_homogenization(homogenization)
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self.set_comments(comments)
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@classmethod
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def from_file(cls,fname):
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"""
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Reads a geom file.
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Parameters
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----------
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||||
fname : str or file handle
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geometry file to read.
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def __repr__(self):
|
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"""Basic information on geometry definition."""
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return util.srepr([
|
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'grid a b c: {}'.format(' x '.join(map(str,self.get_grid ()))),
|
||||
'size x y z: {}'.format(' x '.join(map(str,self.get_size ()))),
|
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'origin x y z: {}'.format(' '.join(map(str,self.get_origin()))),
|
||||
'homogenization: {}'.format(self.get_homogenization()),
|
||||
'# microstructures: {}'.format(len(np.unique(self.microstructure))),
|
||||
'max microstructure: {}'.format(np.nanmax(self.microstructure)),
|
||||
])
|
||||
|
||||
"""
|
||||
with (open(fname) if isinstance(fname,str) else fname) as f:
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||||
f.seek(0)
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||||
header_length,keyword = f.readline().split()[:2]
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||||
header_length = int(header_length)
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||||
content = f.readlines()
|
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def update(self,microstructure=None,size=None,origin=None,rescale=False):
|
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"""
|
||||
Updates microstructure and size.
|
||||
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||||
if not keyword.startswith('head') or header_length < 3:
|
||||
raise TypeError('Header length information missing or invalid')
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||||
Parameters
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||||
----------
|
||||
microstructure : numpy.ndarray, optional
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||||
microstructure array (3D).
|
||||
size : list or numpy.ndarray, optional
|
||||
physical size of the microstructure in meter.
|
||||
origin : list or numpy.ndarray, optional
|
||||
physical origin of the microstructure in meter.
|
||||
rescale : bool, optional
|
||||
ignore size parameter and rescale according to change of grid points.
|
||||
|
||||
comments = []
|
||||
for i,line in enumerate(content[:header_length]):
|
||||
items = line.lower().strip().split()
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||||
key = items[0] if len(items) > 0 else ''
|
||||
if key == 'grid':
|
||||
grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
|
||||
elif key == 'size':
|
||||
size = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
|
||||
elif key == 'origin':
|
||||
origin = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
|
||||
elif key == 'homogenization':
|
||||
homogenization = int(items[1])
|
||||
else:
|
||||
comments.append(line.strip())
|
||||
"""
|
||||
grid_old = self.get_grid()
|
||||
size_old = self.get_size()
|
||||
origin_old = self.get_origin()
|
||||
unique_old = len(np.unique(self.microstructure))
|
||||
max_old = np.nanmax(self.microstructure)
|
||||
|
||||
if size is not None and rescale:
|
||||
raise ValueError('Either set size explicitly or rescale automatically')
|
||||
|
||||
microstructure = np.empty(grid.prod()) # initialize as flat array
|
||||
i = 0
|
||||
for line in content[header_length:]:
|
||||
items = line.split()
|
||||
if len(items) == 3:
|
||||
if items[1].lower() == 'of':
|
||||
items = np.ones(int(items[0]))*float(items[2])
|
||||
elif items[1].lower() == 'to':
|
||||
items = np.linspace(int(items[0]),int(items[2]),
|
||||
abs(int(items[2])-int(items[0]))+1,dtype=float)
|
||||
else: items = list(map(float,items))
|
||||
else: items = list(map(float,items))
|
||||
self.set_microstructure(microstructure)
|
||||
self.set_origin(origin)
|
||||
|
||||
if size is not None:
|
||||
self.set_size(size)
|
||||
elif rescale:
|
||||
self.set_size(self.get_grid()/grid_old*self.size)
|
||||
|
||||
message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))]
|
||||
if np.any(grid_old != self.get_grid()):
|
||||
message[-1] = util.delete(message[-1])
|
||||
message.append(util.emph('grid a b c: {}'.format(' x '.join(map(str,self.get_grid())))))
|
||||
|
||||
message.append('size x y z: {}'.format(' x '.join(map(str,size_old))))
|
||||
if np.any(size_old != self.get_size()):
|
||||
message[-1] = util.delete(message[-1])
|
||||
message.append(util.emph('size x y z: {}'.format(' x '.join(map(str,self.get_size())))))
|
||||
|
||||
message.append('origin x y z: {}'.format(' '.join(map(str,origin_old))))
|
||||
if np.any(origin_old != self.get_origin()):
|
||||
message[-1] = util.delete(message[-1])
|
||||
message.append(util.emph('origin x y z: {}'.format(' '.join(map(str,self.get_origin())))))
|
||||
|
||||
message.append('homogenization: {}'.format(self.get_homogenization()))
|
||||
|
||||
message.append('# microstructures: {}'.format(unique_old))
|
||||
if unique_old != len(np.unique(self.microstructure)):
|
||||
message[-1] = util.delete(message[-1])
|
||||
message.append(util.emph('# microstructures: {}'.format(len(np.unique(self.microstructure)))))
|
||||
|
||||
message.append('max microstructure: {}'.format(max_old))
|
||||
if max_old != np.nanmax(self.microstructure):
|
||||
message[-1] = util.delete(message[-1])
|
||||
message.append(util.emph('max microstructure: {}'.format(np.nanmax(self.microstructure))))
|
||||
|
||||
return util.return_message(message)
|
||||
|
||||
def set_comments(self,comments):
|
||||
"""
|
||||
Replaces all existing comments.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
comments : list of str
|
||||
new comments.
|
||||
|
||||
"""
|
||||
self.comments = []
|
||||
self.add_comments(comments)
|
||||
|
||||
microstructure[i:i+len(items)] = items
|
||||
i += len(items)
|
||||
def add_comments(self,comments):
|
||||
"""
|
||||
Appends comments to existing comments.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
comments : list of str
|
||||
new comments.
|
||||
|
||||
"""
|
||||
self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
|
||||
|
||||
def set_microstructure(self,microstructure):
|
||||
"""
|
||||
Replaces the existing microstructure representation.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
microstructure : numpy.ndarray
|
||||
microstructure array (3D).
|
||||
|
||||
"""
|
||||
if microstructure is not None:
|
||||
if len(microstructure.shape) != 3:
|
||||
raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape))
|
||||
elif microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
|
||||
raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype))
|
||||
else:
|
||||
self.microstructure = np.copy(microstructure)
|
||||
|
||||
def set_size(self,size):
|
||||
"""
|
||||
Replaces the existing size information.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : list or numpy.ndarray
|
||||
physical size of the microstructure in meter.
|
||||
|
||||
"""
|
||||
if size is None:
|
||||
grid = np.asarray(self.microstructure.shape)
|
||||
self.size = grid/np.max(grid)
|
||||
else:
|
||||
if len(size) != 3 or any(np.array(size)<=0):
|
||||
raise ValueError('Invalid size {}'.format(*size))
|
||||
else:
|
||||
self.size = np.array(size)
|
||||
|
||||
def set_origin(self,origin):
|
||||
"""
|
||||
Replaces the existing origin information.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
origin : list or numpy.ndarray
|
||||
physical origin of the microstructure in meter
|
||||
|
||||
"""
|
||||
if origin is not None:
|
||||
if len(origin) != 3:
|
||||
raise ValueError('Invalid origin {}'.format(*origin))
|
||||
else:
|
||||
self.origin = np.array(origin)
|
||||
|
||||
def set_homogenization(self,homogenization):
|
||||
"""
|
||||
Replaces the existing homogenization index.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
homogenization : integer
|
||||
homogenization index
|
||||
|
||||
"""
|
||||
if homogenization is not None:
|
||||
if not isinstance(homogenization,int) or homogenization < 1:
|
||||
raise TypeError('Invalid homogenization {}'.format(homogenization))
|
||||
else:
|
||||
self.homogenization = homogenization
|
||||
|
||||
|
||||
def get_microstructure(self):
|
||||
"""Return the microstructure representation."""
|
||||
return np.copy(self.microstructure)
|
||||
|
||||
def get_size(self):
|
||||
"""Return the physical size in meter."""
|
||||
return np.copy(self.size)
|
||||
|
||||
def get_origin(self):
|
||||
"""Return the origin in meter."""
|
||||
return np.copy(self.origin)
|
||||
|
||||
def get_grid(self):
|
||||
"""Return the grid discretization."""
|
||||
return np.array(self.microstructure.shape)
|
||||
|
||||
def get_homogenization(self):
|
||||
"""Return the homogenization index."""
|
||||
return self.homogenization
|
||||
|
||||
def get_comments(self):
|
||||
"""Return the comments."""
|
||||
return self.comments[:]
|
||||
|
||||
def get_header(self):
|
||||
"""Return the full header (grid, size, origin, homogenization, comments)."""
|
||||
header = ['{} header'.format(len(self.comments)+4)] + self.comments
|
||||
header.append('grid a {} b {} c {}'.format(*self.get_grid()))
|
||||
header.append('size x {} y {} z {}'.format(*self.get_size()))
|
||||
header.append('origin x {} y {} z {}'.format(*self.get_origin()))
|
||||
header.append('homogenization {}'.format(self.get_homogenization()))
|
||||
return header
|
||||
|
||||
@classmethod
|
||||
def from_file(cls,fname):
|
||||
"""
|
||||
Reads a geom file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str or file handle
|
||||
geometry file to read.
|
||||
|
||||
"""
|
||||
with (open(fname) if isinstance(fname,str) else fname) as f:
|
||||
f.seek(0)
|
||||
header_length,keyword = f.readline().split()[:2]
|
||||
header_length = int(header_length)
|
||||
content = f.readlines()
|
||||
|
||||
if not keyword.startswith('head') or header_length < 3:
|
||||
raise TypeError('Header length information missing or invalid')
|
||||
|
||||
comments = []
|
||||
for i,line in enumerate(content[:header_length]):
|
||||
items = line.lower().strip().split()
|
||||
key = items[0] if len(items) > 0 else ''
|
||||
if key == 'grid':
|
||||
grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
|
||||
elif key == 'size':
|
||||
size = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
|
||||
elif key == 'origin':
|
||||
origin = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
|
||||
elif key == 'homogenization':
|
||||
homogenization = int(items[1])
|
||||
else:
|
||||
comments.append(line.strip())
|
||||
|
||||
microstructure = np.empty(grid.prod()) # initialize as flat array
|
||||
i = 0
|
||||
for line in content[header_length:]:
|
||||
items = line.split()
|
||||
if len(items) == 3:
|
||||
if items[1].lower() == 'of':
|
||||
items = np.ones(int(items[0]))*float(items[2])
|
||||
elif items[1].lower() == 'to':
|
||||
items = np.linspace(int(items[0]),int(items[2]),
|
||||
abs(int(items[2])-int(items[0]))+1,dtype=float)
|
||||
else: items = list(map(float,items))
|
||||
else: items = list(map(float,items))
|
||||
microstructure[i:i+len(items)] = items
|
||||
i += len(items)
|
||||
|
||||
if i != grid.prod():
|
||||
raise TypeError('Invalid file: expected {} entries,found {}'.format(grid.prod(),i))
|
||||
|
||||
microstructure = microstructure.reshape(grid,order='F')
|
||||
if not np.any(np.mod(microstructure.flatten(),1) != 0.0): # no float present
|
||||
microstructure = microstructure.astype('int')
|
||||
|
||||
return cls(microstructure.reshape(grid),size,origin,homogenization,comments)
|
||||
|
||||
|
||||
def to_file(self,fname):
|
||||
"""
|
||||
Writes a geom file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str or file handle
|
||||
geometry file to write.
|
||||
|
||||
"""
|
||||
header = self.get_header()
|
||||
grid = self.get_grid()
|
||||
format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure))))) if self.microstructure.dtype == int \
|
||||
else '%g'
|
||||
np.savetxt(fname,
|
||||
self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
|
||||
header='\n'.join(header), fmt=format_string, comments='')
|
||||
|
||||
def to_vtk(self,fname=None):
|
||||
"""
|
||||
Generates vtk file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str, optional
|
||||
vtk file to write. If no file is given, a string is returned.
|
||||
|
||||
"""
|
||||
grid = self.get_grid() + np.ones(3,dtype=int)
|
||||
size = self.get_size()
|
||||
origin = self.get_origin()
|
||||
|
||||
coords = [
|
||||
np.linspace(0,size[0],grid[0]) + origin[0],
|
||||
np.linspace(0,size[1],grid[1]) + origin[1],
|
||||
np.linspace(0,size[2],grid[2]) + origin[2]
|
||||
]
|
||||
|
||||
rGrid = vtk.vtkRectilinearGrid()
|
||||
coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]
|
||||
|
||||
rGrid.SetDimensions(*grid)
|
||||
for d,coord in enumerate(coords):
|
||||
for c in coord:
|
||||
coordArray[d].InsertNextValue(c)
|
||||
|
||||
rGrid.SetXCoordinates(coordArray[0])
|
||||
rGrid.SetYCoordinates(coordArray[1])
|
||||
rGrid.SetZCoordinates(coordArray[2])
|
||||
|
||||
ms = numpy_support.numpy_to_vtk(num_array=self.microstructure.flatten(order='F'),
|
||||
array_type=vtk.VTK_INT if self.microstructure.dtype == int else vtk.VTK_FLOAT)
|
||||
ms.SetName('microstructure')
|
||||
rGrid.GetCellData().AddArray(ms)
|
||||
|
||||
|
||||
if fname is None:
|
||||
writer = vtk.vtkDataSetWriter()
|
||||
writer.SetHeader('damask.Geom '+version)
|
||||
writer.WriteToOutputStringOn()
|
||||
else:
|
||||
writer = vtk.vtkXMLRectilinearGridWriter()
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetDataModeToBinary()
|
||||
|
||||
ext = os.path.splitext(fname)[1]
|
||||
if ext == '':
|
||||
name = fname + '.' + writer.GetDefaultFileExtension()
|
||||
elif ext == writer.GetDefaultFileExtension():
|
||||
name = fname
|
||||
else:
|
||||
raise ValueError("unknown extension {}".format(ext))
|
||||
writer.SetFileName(name)
|
||||
|
||||
if i != grid.prod():
|
||||
raise TypeError('Invalid file: expected {} entries,found {}'.format(grid.prod(),i))
|
||||
|
||||
microstructure = microstructure.reshape(grid,order='F')
|
||||
if not np.any(np.mod(microstructure.flatten(),1) != 0.0): # no float present
|
||||
microstructure = microstructure.astype('int')
|
||||
|
||||
return cls(microstructure.reshape(grid),size,origin,homogenization,comments)
|
||||
writer.SetInputData(rGrid)
|
||||
writer.Write()
|
||||
|
||||
def to_file(self,fname):
|
||||
"""
|
||||
Writes a geom file.
|
||||
if fname is None: return writer.GetOutputString()
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str or file handle
|
||||
geometry file to write.
|
||||
|
||||
"""
|
||||
header = self.get_header()
|
||||
grid = self.get_grid()
|
||||
format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure))))) if self.microstructure.dtype == int \
|
||||
else '%g'
|
||||
np.savetxt(fname,
|
||||
self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
|
||||
header='\n'.join(header), fmt=format_string, comments='')
|
||||
|
||||
def show(self):
|
||||
"""Show raw content (as in file)."""
|
||||
f=StringIO()
|
||||
self.to_file(f)
|
||||
f.seek(0)
|
||||
return ''.join(f.readlines())
|
||||
|
||||
|
||||
|
||||
def to_vtk(self,fname=None):
|
||||
"""
|
||||
Generates vtk file.
|
||||
def mirror(self,directions,reflect=False):
|
||||
"""
|
||||
Mirror microstructure along given directions.
|
||||
Parameters
|
||||
----------
|
||||
directions : iterable containing str
|
||||
direction(s) along which the microstructure is mirrored. Valid entries are 'x', 'y', 'z'.
|
||||
reflect : bool, optional
|
||||
reflect (include) outermost layers.
|
||||
"""
|
||||
valid = {'x','y','z'}
|
||||
if not all(isinstance(d, str) for d in directions):
|
||||
raise TypeError('Directions are not of type str.')
|
||||
elif not set(directions).issubset(valid):
|
||||
raise ValueError('Invalid direction specified {}'.format(*set(directions).difference(valid)))
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str, optional
|
||||
vtk file to write. If no file is given, a string is returned.
|
||||
limits = [None,None] if reflect else [-2,0]
|
||||
ms = self.get_microstructure()
|
||||
|
||||
"""
|
||||
grid = self.get_grid() + np.ones(3,dtype=int)
|
||||
size = self.get_size()
|
||||
origin = self.get_origin()
|
||||
|
||||
coords = [
|
||||
np.linspace(0,size[0],grid[0]) + origin[0],
|
||||
np.linspace(0,size[1],grid[1]) + origin[1],
|
||||
np.linspace(0,size[2],grid[2]) + origin[2]
|
||||
]
|
||||
|
||||
rGrid = vtk.vtkRectilinearGrid()
|
||||
coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]
|
||||
|
||||
rGrid.SetDimensions(*grid)
|
||||
for d,coord in enumerate(coords):
|
||||
for c in coord:
|
||||
coordArray[d].InsertNextValue(c)
|
||||
|
||||
rGrid.SetXCoordinates(coordArray[0])
|
||||
rGrid.SetYCoordinates(coordArray[1])
|
||||
rGrid.SetZCoordinates(coordArray[2])
|
||||
|
||||
ms = numpy_support.numpy_to_vtk(num_array=self.microstructure.flatten(order='F'),
|
||||
array_type=vtk.VTK_INT if self.microstructure.dtype == int else vtk.VTK_FLOAT)
|
||||
ms.SetName('microstructure')
|
||||
rGrid.GetCellData().AddArray(ms)
|
||||
if 'z' in directions:
|
||||
ms = np.concatenate([ms,ms[:,:,limits[0]:limits[1]:-1]],2)
|
||||
if 'y' in directions:
|
||||
ms = np.concatenate([ms,ms[:,limits[0]:limits[1]:-1,:]],1)
|
||||
if 'x' in directions:
|
||||
ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
|
||||
|
||||
return self.update(ms,rescale=True)
|
||||
#self.add_comments('tbd')
|
||||
|
||||
|
||||
if fname is None:
|
||||
writer = vtk.vtkDataSetWriter()
|
||||
writer.SetHeader('damask.Geom '+version)
|
||||
writer.WriteToOutputStringOn()
|
||||
else:
|
||||
writer = vtk.vtkXMLRectilinearGridWriter()
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetDataModeToBinary()
|
||||
|
||||
ext = os.path.splitext(fname)[1]
|
||||
if ext == '':
|
||||
name = fname + '.' + writer.GetDefaultFileExtension()
|
||||
elif ext == writer.GetDefaultFileExtension():
|
||||
name = fname
|
||||
else:
|
||||
raise ValueError("unknown extension {}".format(ext))
|
||||
writer.SetFileName(name)
|
||||
|
||||
writer.SetInputData(rGrid)
|
||||
writer.Write()
|
||||
def clean(self,stencil=3):
|
||||
"""
|
||||
Smooth microstructure by selecting most frequent index within given stencil at each location.
|
||||
Parameters
|
||||
----------
|
||||
stencil : int, optional
|
||||
size of smoothing stencil.
|
||||
"""
|
||||
def mostFrequent(arr):
|
||||
unique, inverse = np.unique(arr, return_inverse=True)
|
||||
return unique[np.argmax(np.bincount(inverse))]
|
||||
|
||||
if fname is None: return writer.GetOutputString()
|
||||
|
||||
|
||||
def show(self):
|
||||
"""Show raw content (as in file)."""
|
||||
f=StringIO()
|
||||
self.to_file(f)
|
||||
f.seek(0)
|
||||
return ''.join(f.readlines())
|
||||
return self.update(ndimage.filters.generic_filter(self.microstructure,
|
||||
mostFrequent,
|
||||
size=(stencil,)*3).astype(self.microstructure.dtype))
|
||||
#self.add_comments('tbd')
|
||||
|
|
|
|||
Loading…
Reference in New Issue